def environment_selection(self, args):
v_list = []
indi_list = []
for indi in self.pops.individuals:
indi_list.append(indi)
v_list.append(indi.acc)
for indi in self.parent_pops.individuals:
indi_list.append(indi)
v_list.append(indi.acc)
#add log
# find the largest one's index
max_index = np.argmax(v_list)
selection = Selection()
selected_index_list = selection.RouletteSelection(v_list, k=args.pop_size)
if max_index not in selected_index_list:
first_selectd_v_list = [v_list[i] for i in selected_index_list]
min_idx = np.argmin(first_selectd_v_list)
selected_index_list[min_idx] = max_index
next_individuals = [indi_list[i] for i in selected_index_list]
next_gen_pops = Population(args, self.pops.gen_no+1)
next_gen_pops.create_from_offspring(next_individuals)
self.pops = next_gen_pops
def initialize_population(self):
'''
种群初始化
'''
# utils 中.ini [IS_RUNNING] 参数置1
StatusUpdateTool.begin_evolution()
pops = Population(params, 0)
pops.initialize()
self.pops = pops
Utils.save_population_at_begin(str(pops), 0)
def initialize_population(self):
'''
种群初始化
'''
# ini文件IS_RUNNING参数置1
StatusUpdateTool.begin_evolution()
# 初始化种群，传入ini文件的参数
pops = Population(params, 0)
pops.initialize()
self.pops = pops
# 建立并写入种群begin文件
Utils.save_population_at_begin(str(pops), 0)
def do_genetic(population, population_propogation_function):
iterations = 0
last_n = [float('Inf')] * Params.stop_genetic_after_count
best_gene = None
while True:
iterations += 1
max_evaluation = population.get_max_evaluation(graph)
last_n.pop(0)
last_n.append(max_evaluation)
flag = False
for i in range(len(last_n)):
if i != 0 and last_n[i] != last_n[i - 1]:
flag = True
if not flag:
break
print(max_evaluation)
best_gene = population.best_n(1, graph)[0]
print(best_gene)
if Params.show_plot:
plot_figure(best_gene, graph)
new_population = population_propogation_function(population, graph)
population = Population(new_population)
Graph.no_colours = len(set(best_gene.array))
eval = best_gene.evaluate(graph)
no_colors = len(set(best_gene.array))
conflicts = -1 * (eval + (no_colors * Params.penalty_per_color_used)
) / Params.penalty_same_color
return iterations, best_gene, conflicts
def environment_selection(self):
v_list = []
indi_list = []
# 将此时的种群acc和父种群acc记录在一起
for indi in self.pops.individuals:
indi_list.append(indi)
v_list.append(indi.acc)
for indi in self.parent_pops.individuals:
indi_list.append(indi)
v_list.append(indi.acc)
_str = []
for _, indi in enumerate(self.pops.individuals):
_t_str = 'Indi-%s-%.5f-%s' % (indi.id, indi.acc, indi.uuid()[0])
_str.append(_t_str)
for _, indi in enumerate(self.parent_pops.individuals):
_t_str = 'Pare-%s-%.5f-%s' % (indi.id, indi.acc, indi.uuid()[0])
_str.append(_t_str)
# add log
# find the largest one's index
# 选出max个体并筛选下一代
max_index = np.argmax(v_list)
selection = Selection()
# 采用轮盘赌选择算法
selected_index_list = selection.RouletteSelection(
v_list, k=self.params['pop_size'])
if max_index not in selected_index_list:
# 若max个体不在筛选结果中，那么从筛选结果中替换掉其中的min个体
first_selectd_v_list = [v_list[i] for i in selected_index_list]
min_idx = np.argmin(first_selectd_v_list)
selected_index_list[min_idx] = max_index
next_individuals = [indi_list[i] for i in selected_index_list]
"""Here, the population information should be updated, such as the gene no and then to the individual id"""
# 更新种群基本信息
next_gen_pops = Population(self.pops.params, self.pops.gen_no + 1)
next_gen_pops.create_from_offspring(next_individuals)
self.pops = next_gen_pops
for _, indi in enumerate(self.pops.individuals):
_t_str = 'new -%s-%.5f-%s' % (indi.id, indi.acc, indi.uuid()[0])
_str.append(_t_str)
_file = './populations/ENVI_%2d.txt' % (self.pops.gen_no)
Utils.write_to_file('\n'.join(_str), _file)
Utils.save_population_at_begin(str(self.pops), self.pops.gen_no)
def __init__(self, screen, size):
# Display attributes
self.screen = screen
self.size = size
self.font = pygame.font.Font('ressources/font/DroidSansMono.ttf', 20)
self.font_small = pygame.font.Font('ressources/font/DroidSansMono.ttf',
12)
# Genetic attributes
self.training_enabled = False
self.pop = Population()
self.pool = [] # The population of individuals
self.gen_number = 1 # The generation number
self.best_score = 0 # The best score for an individual
# pop scores.
self.best_pop_score = 0
self.gens_without_hs = 0
def create_population(individual_num, genes_num):
'''
Creates a new population.
individual_num:
Number of individuals of the population.
genes_num:
Number of genes of each individual.
'''
individual_list = []
for i in range(individual_num):
individual = create_individual(genes_num)
individual_list.append(individual)
return Population(individuals=individual_list)
def get_next_population(current_population, mutator, fitnessFunction):
'''
Generates the next new population.
The new population is composed by the fittest genes of the current population.
'''
individual_list = current_population.individuals
next_individual_list = []
next_individual_list.append(individual_list[0])
while len(next_individual_list) < len(individual_list):
parent1, i = pick_individual(individual_list, -1)
parent2, i = pick_individual(individual_list, i)
next_individual = reproduce(parent1, parent2, mutator)
next_individual_list.append(next_individual)
next_individual_list = sorted(next_individual_list, key=lambda individual: fitnessFunction.calculate_fitness(individual), reverse=True)
return Population(individuals=next_individual_list)
def load_population(cls, prefix, gen_no):
'''
读取 .txt 文件，解析字符串
'''
file_name = './populations/%s_%02d.json' % (prefix, np.min(gen_no))
params = StatusUpdateTool.get_init_params()
pop = Population(params, gen_no)
f = open(file_name, 'r')
# *** strip() 方法用于移除字符串头尾指定的字符（默认为空格或换行符）或字符序列。
info = json.load(f)
# individuals = info["populations"]
for i in info["populations"]:
individual_item = info
individual_item["net"] = i
indi_no = i["indi_no"]
indi = Individual(individual_item, indi_no)
# indi_no = indi_start_line[5:]
# indi = Individual(params, indi_no)
pop.individuals.append(indi)
f.close()
# load the fitness to the individuals who have been evaluated, only suitable for the first generation
if gen_no == 0:
after_file_path = './populations/after_%02d.json' % (gen_no)
if os.path.exists(after_file_path):
# 从after_文件中取出已训练好的accuracy数据
fitness_map = {}
f = open(after_file_path, 'r')
info = json.load(f)
for i in info["populations"]:
if "accuracy" in i:
fitness_map[i["indi_no"]] = i["accuracy"]
f.close()
for indi in pop.individuals:
if indi.id in fitness_map:
indi.acc = fitness_map[indi.id]
return pop
class Genetic:
def __init__(self, screen, size):
# Display attributes
self.screen = screen
self.size = size
self.font = pygame.font.Font('ressources/font/DroidSansMono.ttf', 20)
self.font_small = pygame.font.Font('ressources/font/DroidSansMono.ttf',
12)
# Genetic attributes
self.training_enabled = False
self.pop = Population()
self.pool = [] # The population of individuals
self.gen_number = 1 # The generation number
self.best_score = 0 # The best score for an individual
# pop scores.
self.best_pop_score = 0
self.gens_without_hs = 0
# Enable or disable the training.
def toggle_training(self, enabled):
if enabled:
self.training_enabled = True
else:
self.training_enabled = False
# Create a default population of stupid bunnies.
def init(self):
# Create a default population.
self.pop.create_default_pop()
self.pool = self.pop.population
# Reset the pool
def next_pop(self):
# Get the last gen survivor
best_individual = self.pop.get_best_individual(self.pool)
# Count how many gens could not improve the high score.
if self.best_pop_score < best_individual.score:
self.best_pop_score = best_individual.score
self.gens_without_hs = 0
else:
self.gens_without_hs += 1
# Reset the pool.
self.pool = []
self.gen_number += 1
# Prepare next population.
self.pop.breed(best_individual,
self.stupidity_factor(self.gens_without_hs))
self.pool = self.pop.population
# Define the supidity factor of a pop depending on how many gens didn't beat high score.
def stupidity_factor(self, gens_without_hs):
if gens_without_hs == 5:
print('Population is maybe stupid')
if gens_without_hs > 10:
print('Population is really stupid')
# Maybe tweak this return result.
return gens_without_hs
def gen_watcher(self):
best_individual = self.pop.get_best_individual(self.pool)
# Display population data
self.display_gen_data(best_individual.score)
# Display the neural network
self.display_neural_network(best_individual)
def think(self, player, display):
# Get the inputs.
inputs = self.get_inputs(player, display)
# Feed the inputs to a function
determined_output = self.determine_output(inputs, player)
# print(determined_output)
if determined_output > 0.5:
self.output_jump(player)
# From 0 to 1
def determine_output(self, inputs, player):
# The 4 inputs
i1 = int(inputs[0])
i2 = int(inputs[1])
i3 = inputs[2]
i4 = inputs[3]
# Inputs to layer weights
w_i1_j1 = player.synapses[0]
w_i1_j2 = player.synapses[1]
w_i1_j3 = player.synapses[2]
w_i1_j4 = player.synapses[3]
w_i2_j1 = player.synapses[2]
w_i2_j2 = player.synapses[3]
w_i2_j3 = player.synapses[4]
w_i2_j4 = player.synapses[5]
w_i3_j1 = player.synapses[4]
w_i3_j2 = player.synapses[5]
w_i3_j3 = player.synapses[6]
w_i3_j4 = player.synapses[7]
w_i4_j1 = player.synapses[6]
w_i4_j2 = player.synapses[7]
w_i4_j3 = player.synapses[8]
w_i4_j4 = player.synapses[9]
# Layer to output weights
w_j1_k1 = player.synapses[10]
w_j2_k1 = player.synapses[11]
w_j3_k1 = player.synapses[12]
w_j4_k1 = player.synapses[13]
bias = 2
j1 = player.sigmoid((i1 * w_i1_j1 + i2 * w_i2_j1 + i3 * w_i3_j1 +
i4 * w_i4_j1) + bias)
j2 = player.sigmoid((i1 * w_i1_j2 + i2 * w_i2_j2 + i3 * w_i3_j2 +
i4 * w_i4_j2) + bias)
j3 = player.sigmoid((i1 * w_i1_j3 + i2 * w_i2_j3 + i3 * w_i3_j3 +
i4 * w_i4_j3) + bias)
j4 = player.sigmoid((i1 * w_i1_j4 + i2 * w_i2_j4 + i3 * w_i3_j4 +
i4 * w_i4_j4) + bias)
k1 = j1 * w_j1_k1 + j2 * w_j2_k1 + j3 * w_j3_k1 + j4 * w_j4_k1
return player.sigmoid(k1)
# player status, obstacle distances.
def get_inputs(self, player, display):
obstacles = display.om.get_obstacles()
obstacle_positions = self.get_obstacle_positions(obstacles)
# We need to know the distance from the first obstacle
if len(obstacle_positions) > 0:
next_obstacle_dist = obstacle_positions[0] - (player.pos_x +
player.size_x)
else:
next_obstacle_dist = 1
# We need to know how far is the next obstacle
if len(obstacle_positions) > 1:
obstacle_spacing = obstacle_positions[1] - obstacle_positions[0]
else:
obstacle_spacing = 1
jump_fall = 0
obstacle_spacing = 0
if player.jumping:
if player.falling:
jump_fall = 1
inputs = [
jump_fall, # If player is already jumping
player.pos_y,
next_obstacle_dist, # The distance between the player and next obstacle
obstacle_spacing, # The spacing between 1st and 2nd obstacle
]
return inputs
# Get the x coords of obstacles.
def get_obstacle_positions(self, obstacles):
obstacles_pos = []
for obstacle in obstacles:
obstacles_pos.append(obstacle.pos_x)
return obstacles_pos
# Make the bunny jump.
def output_jump(self, individual):
individual.do_jump()
# Use the om from display to reset obstacles.
def reset_obstacles(self, display):
display.om.clear_all_obstacles()
def display_gen_data(self, player_score):
color = 255, 171, 0
# Display alive individuals.
gen_string = 'Bunnies alive : {:05d}'.format(len(self.pool))
text = self.font.render(gen_string, True, color)
text_rect = text.get_rect()
text_rect.top = 20
text_rect.right = self.size[0] - 20
self.screen.blit(text, text_rect)
# Display current gen.
gen_string = 'Generation : {:05d}'.format(self.gen_number)
text = self.font.render(gen_string, True, color)
text_rect = text.get_rect()
text_rect.top = 40
text_rect.right = self.size[0] - 20
self.screen.blit(text, text_rect)
# Display the best score an individual could achieve.
if player_score > self.best_score:
self.best_score = player_score
gen_string = 'Best Score : {:05d}'.format(self.best_score)
text = self.font.render(gen_string, True, color)
text_rect = text.get_rect()
text_rect.top = 60
text_rect.right = self.size[0] - 20
self.screen.blit(text, text_rect)
gen_string = 'Stupidity factor : {:05d}'.format(self.gens_without_hs)
text = self.font.render(gen_string, True, color)
text_rect = text.get_rect()
text_rect.top = 80
text_rect.right = self.size[0] - 20
self.screen.blit(text, text_rect)
# Display the neural network of an individual. (the best in this case)
def display_neural_network(self, player):
green = 0, 170, 0
white = 255, 255, 255
black = 0, 0, 0
red = 255, 0, 0
orange = 230, 82, 0
i1_pos = (30, 30)
i2_pos = (30, 70)
i3_pos = (30, 110)
i4_pos = (30, 150)
j1_pos = (120, 30)
j2_pos = (120, 70)
j3_pos = (120, 110)
j4_pos = (120, 150)
k1_pos = (160, 90)
circles = [
i1_pos, # I1
i2_pos, # I2
i3_pos, # I3
i4_pos, # I4
j1_pos, # J1
j2_pos, # J2
j3_pos, # J3
j4_pos, # J4
k1_pos, # K1
]
# Draw circles
for circle in circles:
pygame.draw.circle(self.screen, (255, 255, 255), circle, 8, 1)
# Build lines data
lines = []
for synapse in player.synapses:
if synapse > 2:
color = white
elif synapse > 0:
color = green
elif synapse > -1:
color = orange
elif synapse > -2:
color = red
else:
color = black
lines.append(color)
lines_coord = [
# Lines from i1
[i1_pos, j1_pos], # w_i1_j1
[i1_pos, j2_pos], # w_i1_j2
[i1_pos, j3_pos], # w_i1_j3
[i1_pos, j4_pos], # w_i1_j4
# Lines from i2
[i2_pos, j1_pos], # w_i2_j1
[i2_pos, j2_pos], # w_i2_j2
[i2_pos, j3_pos], # w_i2_j3
[i2_pos, j4_pos], # w_i2_j4
# Lines from i3
[i3_pos, j1_pos], # w_i3_j1
[i3_pos, j2_pos], # w_i3_j2
[i3_pos, j3_pos], # w_i3_j3
[i3_pos, j4_pos], # w_i3_j4
# Lines from i4
[i4_pos, j1_pos], # w_i4_j1
[i4_pos, j2_pos], # w_i4_j2
[i4_pos, j3_pos], # w_i4_j3
[i4_pos, j4_pos], # w_i4_j4
# Lines from J layer to K
[j1_pos, k1_pos], # w_j1_k1
[j2_pos, k1_pos], # w_j2_k1
[j3_pos, k1_pos], # w_j3_k1
[j4_pos, k1_pos], # w_j4_k1
]
# Draw lines
i = 0
for line in lines:
pygame.draw.line(self.screen, line, lines_coord[i][0],
lines_coord[i][1], 2)
i += 1
def initialize_population(self, args):
pops = Population(args, 0)
pops.re_initialize(args)
self.pops = pops
}
evaluator = ANNCoverageEvaluator(**evaluator_args)
population_args = {
"pop_size": POP_SIZE,
"genome_size": evaluator.get_genome_size(),
"eval_func": evaluator.evaluate,
"init_func": np.random.normal,
"weight_scale": 1.0,
"mutation_rate": 0.1,
"mutation_scale": 0.1,
"selection_rate": 0.9
}
population = Population(pop_size=population_args["pop_size"],
genome_size=population_args["genome_size"],
eval_func=population_args["eval_func"],
mutation_rate=population_args["mutation_rate"],
mutation_scale=population_args["mutation_scale"],
init_func=np.random.normal)
# Train
iterations = 200
# ann, history = train(iterations=iterations, generator=generator, evaluator=evaluator, population=population)
ann, history = train(iterations=iterations,
generator=generator,
evaluator=evaluator,
population=population,
world_name=world_name,
evaluator_args=evaluator_args,
population_args=population_args)
g = visualize.show_history(history)
def initialize_population(self):
StatusUpdateTool.begin_evolution()
pops = Population(params, 0)
pops.initialize()
self.pops = pops
Utils.save_population_at_begin(str(pops), 0)
bot = Bot(settings.BOT_SKINS[0], 75, 200, 300, 290, "Bot")
obs_player = Observer(player, [wall])
obs_bot = Observer(bot, [wall])
player.obs = obs_player
bot.set_target(wall)
bot.obs = obs_bot
_game.player = player
_game.add_object(bot)
if __name__ == "__main__":
pygame.display.set_caption("Smart Square")
game = Game(400, 500)
wall = Wall(settings.SKINS[0], -100, 500, 250, "Wall")
wall.game = game
game.add_object(wall)
# ------------------------------------------------------------
env = Environment()
env.population = Population(10, 0.2)
ai_list, env.observers = create_ai(env.population, target=wall)
game.objects.extend(ai_list)
game.env = env
# ------------------------------------------------------------
game.start()
df = pd.DataFrame({"fitness": fitness, "diversity": diversity})
df["Generation"] = df.index
df = pd.melt(df,
id_vars=['Generation'],
value_vars=["fitness", "diversity"])
return df
if __name__ == "__main__":
functions = [rosenbrock, rastrigin]
function_num = 1
fn = functions[function_num]
population = Population(
100,
2,
lambda x: -fn(x),
mutation_scale=0.2,
init_func=lambda size: np.random.uniform(low=-2, high=2, size=size))
history = evolve(100, population)
df = process_history(history)
g = sns.FacetGrid(data=df, row="variable", height=3, sharey="row")
g = g.map(plt.plot, "Generation", "value")
# sns.lineplot(data=df, x="Generation", y="value", hue="variable")
plt.show()
extent = [-2, 2, -2, 2]
file_name = "ae"
img_dir = ""
if (function_num == 0):
def initialize_population():
n = Params.initial_population_size
population = []
for i in range(n):
population.append(get_random_parent(Graph.no_colours, no_points))
return Population(population)
def load_population(cls, prefix, gen_no):
file_name = './populations/%s_%02d.txt' % (prefix, np.min(gen_no))
params = StatusUpdateTool.get_init_params()
pop = Population(params, gen_no)
f = open(file_name)
indi_start_line = f.readline().strip()
while indi_start_line.startswith('indi'):
indi_no = indi_start_line[5:]
indi = Individual(params, indi_no)
for line in f:
line = line.strip()
if line.startswith('--'):
indi_start_line = f.readline().strip()
break
else:
if line.startswith('Acc'):
indi.acc = float(line[4:])
elif line.startswith('[conv'):
data_maps = line[6:-1].split(',', 5)
conv_params = {}
for data_item in data_maps:
_key, _value = data_item.split(":")
if _key == 'number':
indi.number_id = int(_value)
conv_params['number'] = int(_value)
elif _key == 'in':
conv_params['in_channel'] = int(_value)
elif _key == 'out':
conv_params['out_channel'] = int(_value)
else:
raise ValueError(
'Unknown key for load conv unit, key_name:%s'
% (_key))
conv = ResUnit(conv_params['number'],
conv_params['in_channel'],
conv_params['out_channel'])
indi.units.append(conv)
elif line.startswith('[pool'):
pool_params = {}
for data_item in line[6:-1].split(','):
_key, _value = data_item.split(':')
if _key == 'number':
indi.number_id = int(_value)
pool_params['number'] = int(_value)
elif _key == 'type':
pool_params['max_or_avg'] = float(_value)
else:
raise ValueError(
'Unknown key for load pool unit, key_name:%s'
% (_key))
pool = PoolUnit(pool_params['number'],
pool_params['max_or_avg'])
indi.units.append(pool)
else:
print(
'Unknown key for load unit type, line content:%s' %
(line))
pop.individuals.append(indi)
f.close()
# load the fitness to the individuals who have been evaluated, only suitable for the first generation
if gen_no == 0:
after_file_path = './populations/after_%02d.txt' % (gen_no)
if os.path.exists(after_file_path):
fitness_map = {}
f = open(after_file_path)
for line in f:
if len(line.strip()) > 0:
line = line.strip().split('=')
fitness_map[line[0]] = float(line[1])
f.close()
for indi in pop.individuals:
if indi.id in fitness_map:
indi.acc = fitness_map[indi.id]
return pop
sort_a = a[idx]
sum_a = np.sum(a).astype(np.float)
selected_index = []
for i in range(k):
u = np.random.rand() * sum_a
sum_ = 0
for i in range(sort_a.shape[0]):
sum_ += sort_a[i]
if sum_ > u:
selected_index.append(idx[i])
break
return selected_index[0]
if __name__ == '__main__':
from genetic.population import Population
import logging
FORMAT = '%(asctime)-15s [%(levelname)s] %(message)s'
logging.basicConfig(format=FORMAT, level=logging.DEBUG)
_params = StatusUpdateTool.get_init_params()
_gen_no = 20
pop = Population(_params, _gen_no)
pop.initialize()
_prob = 0.2 # Mutation Probability
m = Mutation(pop.individuals, _prob, logging)
m.do_mutation()
